run_ogrdbstats_tests

#!/bin/sh

cd /data/ogrdb_extdata

Rscript /usr/local/bin/ogrdbstats.R --inf_file novel_gapped.fasta ref_gapped.fasta Homosapiens ogrdbstats_example_repertoire.tsv IGHV

rv=$?  
if [[ $rv != 0 ]]  
then    
    echo "Test failed."  
    exit 1	
fi

if [ ! -f "repertoire_ogrdb_report.csv" ]; then
    echo "Report not created."
	exit 1
fi

diff model_ogrdbstats_example_repertoire_ogrdb_report.csv ogrdbstats_example_repertoire_ogrdb_report.csv

rv=$?  
if [[ $rv != 0 ]]  
then    
    echo "Report does not match expected content"  
    exit 1	
fi

if [ ! -f "repertoire_ogrdb_plots.pdf" ]; then
    echo "PDF not created."
	exit 1
fi

echo "Test passed."
exit 0